catabolism of small carbon sources in Clostridium kluyveri DSM 555

GapMind for catabolism of small carbon sources

catabolism of small carbon sources in Clostridium kluyveri DSM 555

Pathways are sorted by completeness. Sort by name instead.

Pathway	Steps
ethanol	etoh-dh-nad, adh, ackA, pta
alanine	cycA
threonine	serP1, ltaE, adh, ackA, pta, gcvP, gcvT, gcvH, lpd
serine	serP, sdhA, sdhB
D-serine	cycA, dsdA
L-malate	mleP
asparagine	ansP, ans
deoxyinosine	nupC, deoD, deoB, deoC, adh, ackA, pta
thymidine	nupG, deoA, deoB, deoC, adh, ackA, pta
tryptophan	trpP, ecfA1, ecfA2, ecfT, tnaA
deoxyribose	deoP, deoK, deoC, adh, ackA, pta
acetate	actP, ackA, pta
citrate	SLC13A5, acn, icd
maltose	MAL11, susB, glk
D-alanine	cycA, dadA
glucose	MFS-glucose, glk
glutamate	gltS, aspA
D-lactate	lctP, D-LDH
L-lactate	lctP, L-LDH
mannitol	mtlA, mtlD
proline	opuBA, opuBB, put1, putA
trehalose	treEIIA, treB, treC, glk
cellobiose	cdt, cbp, pgmA, glk
fructose	fruII-ABC, 1pfk, fba, tpi
aspartate	glt
fumarate	dctA
glucose-6-P	uhpT
2-oxoglutarate	kgtP
pyruvate	SLC5A8
succinate	sdc
mannose	manP, manA
arginine	rocE, adiA, speB, patA, patD, gabT, gabD
isoleucine	livF, livG, livJ, livH, livM, ofo, acdH, ech, ivdG, fadA, pco, hpcD, dddA, iolA
leucine	livF, livG, livJ, livH, livM, ilvE, ofo, liuA, liuB, liuD, liuC, liuE, aacS, atoB
glycerol	glpF, dhaD, dhaK, dhaL, dhaM, tpi
sucrose	ams, MFS-glucose, glk
galactose	galP, galK, galT, galE, pgmA
glucosamine	gamP, nagB
ribose	rbsU, rbsK
sorbitol	mtlA, srlD
xylitol	fruI, x5p-reductase
lysine	lysP, davB, davA, davT, davD, gcdG, gcdH, ech, fadB, atoB
lactose	lacP, lacZ, galK, galT, galE, pgmA, glk
putrescine	puuP, patA, patD, gabT, gabD
gluconate	gntT, gntK, gnd
NAG	nagEcba, nagA, nagB
xylose	xylT, xylA, xylB
histidine	PA5503, PA5504, PA5505, hutH, hutU, hutI, hutG
valine	livF, livG, livJ, livH, livM, ofo, acdH, ech, bch, mmsB, mmsA, pco, hpcD, dddA, iolA
propionate	putP, prpE, pco, hpcD, dddA, iolA
arabinose	araE, araA, araB, araD
4-hydroxybenzoate	pcaK, pobA, praA, xylF, mhpD, mhpE, adh, ackA, pta
deoxyribonate	deoxyribonate-transport, deoxyribonate-dehyd, ketodeoxyribonate-cleavage, garK, aacS, atoB
tyrosine	aroP, HPD, hmgA, maiA, fahA, aacS, atoB
glucuronate	exuT, udh, gci, kdgD, dopDH
rhamnose	rhaT, LRA1, LRA2, LRA3, LRA5, LRA6
citrulline	AO353_03055, AO353_03050, AO353_03045, AO353_03040, arcB, arcC, rocD, PRO3, put1, putA
fucose	fucP, fucU, fucI, fucK, fucA, tpi, aldA
galacturonate	exuT, uxaC, uxaB, uxaA, kdgK, eda
phenylalanine	aroP, ARO8, iorAB, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2
myoinositol	iolT, iolG, iolE, iolD, iolB, iolC, iolJ, mmsA, tpi
phenylacetate	H281DRAFT_04042, paaK, paaA, paaB, paaC, paaE, paaG, paaZ1, paaZ2, paaJ1, paaF, paaH, paaJ2

Confidence: high confidence medium confidence low confidence
transporter – transporters and PTS systems are shaded because predicting their specificity is particularly challenging.

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

Downloads

Candidates (tab-delimited)
Steps (tab-delimited)
Rules (tab-delimited)
Protein sequences (fasta format)
Organisms (tab-delimited)
SQLite3 databases

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

ublast finds a hit to a characterized protein at above 40% identity and 80% coverage, and bits >= other bits+10.
- (Hits to curated proteins without experimental data as to their function are never considered high confidence.)
HMMer finds a hit with 80% coverage of the model, and either other identity < 40 or other coverage < 0.75.

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

ublast finds a hit at above 40% identity and 70% coverage (ignoring otherBits).
ublast finds a hit at above 30% identity and 80% coverage, and bits >= other bits.
HMMer finds a hit (regardless of coverage or other bits).

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

our ignorance of proteins' functions,
omissions in the gene models,
frame-shift errors in the genome sequence, or
the organism lacks the pathway.

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

the paper from 2019 on GapMind for amino acid biosynthesis
the paper from 2022 on GapMind for carbon sources
the source code
instructions for running GapMind on your computer

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory

GapMind for catabolism of small carbon sources